1
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Ishikawa T, Domergue F, Amato A, Corellou F. Characterization of Unique Eukaryotic Sphingolipids with Temperature-Dependent Δ8-Unsaturation from the Picoalga Ostreococcus tauri. PLANT & CELL PHYSIOLOGY 2024; 65:1029-1046. [PMID: 38252418 DOI: 10.1093/pcp/pcae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/28/2023] [Accepted: 01/18/2024] [Indexed: 01/23/2024]
Abstract
Sphingolipids (SLs) are ubiquitous components of eukaryotic cell membranes and are found in some prokaryotic organisms and viruses. They are composed of a sphingoid backbone that may be acylated and glycosylated. Assembly of various sphingoid base, fatty acyl and glycosyl moieties results in highly diverse structures. The functional significance of variations in SL chemical diversity and abundance is still in the early stages of investigation. Among SL modifications, Δ8-desaturation of the sphingoid base occurs only in plants and fungi. In plants, SL Δ8-unsaturation is involved in cold hardiness. Our knowledge of the structure and functions of SLs in microalgae lags far behind that of animals, plants and fungi. Original SL structures have been reported from microalgae. However, functional studies are still missing. Ostreococcus tauri is a minimal microalga at the base of the green lineage and is therefore a key organism for understanding lipid evolution. In the present work, we achieved the detailed characterization of O. tauri SLs and unveiled unique glycosylceramides as sole complex SLs. The head groups are reminiscent of bacterial SLs, as they contain hexuronic acid residues and can be polyglycosylated. Ceramide backbones show a limited variety, and SL modification is restricted to Δ8-unsaturation. The Δ8-SL desaturase from O. tauri only produced E isomers. Expression of both Δ8-SL desaturase and Δ8-unsaturation of sphingolipids varied with temperature, with lower levels at 24°C than at 14°C. Overexpression of the Δ8-SL desaturase dramatically increases the level of Δ8 unsaturation at 24°C and is paralleled by a failure to increase cell size. Our work provides the first characterization of O. tauri SLs and functional evidence for the involvement of SL Δ8-unsaturation for temperature acclimation in microalgae, suggesting that this function is an ancestral feature in the green lineage.
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Affiliation(s)
- Toshiki Ishikawa
- Graduate School of Science and Engineering, Saitama University, 225 Shimo-Okubo, Sakura-ku, Saitama-city, Saitama, 338-8570 Japan
| | - Frédéric Domergue
- Laboratoire de Biogenèse Membranaire, University of Bordeaux, CNRSUMR 5200, Av. Edouard Bourlaux, Villenave d'Ornon 33140, France
| | - Alberto Amato
- Laboratoire de Physiologie Végétale et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique UMR 5168, Université Grenoble Alpes, CEA, IRIG, 17 Av. Des Martyrs, Grenoble 38000, France
| | - Florence Corellou
- Laboratoire de Physiologie Végétale et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique UMR 5168, Université Grenoble Alpes, CEA, IRIG, 17 Av. Des Martyrs, Grenoble 38000, France
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2
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Foresi N, De Marco MA, Del Castello F, Ramirez L, Nejamkin A, Calo G, Grimsley N, Correa-Aragunde N, Martínez-Noël GMA. The tiny giant of the sea, Ostreococcus's unique adaptations. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108661. [PMID: 38735153 DOI: 10.1016/j.plaphy.2024.108661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 04/14/2024] [Accepted: 04/23/2024] [Indexed: 05/14/2024]
Abstract
Ostreococcus spp. are unicellular organisms with one of the simplest cellular organizations. The sequencing of the genomes of different Ostreococcus species has reinforced this status since Ostreococcus tauri has one most compact nuclear genomes among eukaryotic organisms. Despite this, it has retained a number of genes, setting it apart from other organisms with similar small genomes. Ostreococcus spp. feature a substantial number of selenocysteine-containing proteins, which, due to their higher catalytic activity compared to their selenium-lacking counterparts, may require a reduced quantity of proteins. Notably, O. tauri encodes several ammonium transporter genes, that may provide it with a competitive edge for acquiring nitrogen (N). This characteristic makes it an intriguing model for studying the efficient use of N in eukaryotes. Under conditions of low N availability, O. tauri utilizes N from abundant proteins or amino acids, such as L-arginine, similar to higher plants. However, the presence of a nitric oxide synthase (L-arg substrate) sheds light on a new metabolic pathway for L-arg in algae. The metabolic adaptations of O. tauri to day and night cycles offer valuable insights into carbon and iron metabolic configuration. O. tauri has evolved novel strategies to optimize iron uptake, lacking the classic components of the iron absorption mechanism. Overall, the cellular and genetic characteristics of Ostreococcus contribute to its evolutionary success, making it an excellent model for studying the physiological and genetic aspects of how green algae have adapted to the marine environment. Furthermore, given its potential for lipid accumulation and its marine habitat, it may represent a promising avenue for third-generation biofuels.
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Affiliation(s)
- Noelia Foresi
- Instituto de Investigaciones Biológicas-UNMdP-CONICET, Mar del Plata, Argentina.
| | - María Agustina De Marco
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC)-CONICET-FIBA, Mar del Plata, Argentina
| | | | - Leonor Ramirez
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, SE-901 87, Umeå, Sweden
| | - Andres Nejamkin
- Instituto de Investigaciones Biológicas-UNMdP-CONICET, Mar del Plata, Argentina
| | - Gonzalo Calo
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC)-CONICET-FIBA, Mar del Plata, Argentina
| | - Nigel Grimsley
- CNRS, LBBM, Sorbonne Université OOB, 1 Avenue de Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | | | - Giselle M A Martínez-Noël
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC)-CONICET-FIBA, Mar del Plata, Argentina.
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3
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Rodríguez SG, Crosby P, Hansen LL, Grünewald E, Beale AD, Spangler RK, Rabbitts BM, Partch CL, Stangherlin A, O’Neill JS, van Ooijen G. Potassium rhythms couple the circadian clock to the cell cycle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587153. [PMID: 38617352 PMCID: PMC11014554 DOI: 10.1101/2024.04.02.587153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Circadian (~24 h) rhythms are a fundamental feature of life, and their disruption increases the risk of infectious diseases, metabolic disorders, and cancer1-6. Circadian rhythms couple to the cell cycle across eukaryotes7,8 but the underlying mechanism is unknown. We previously identified an evolutionarily conserved circadian oscillation in intracellular potassium concentration, [K+]i9,10. As critical events in the cell cycle are regulated by intracellular potassium11,12, an enticing hypothesis is that circadian rhythms in [K+]i form the basis of this coupling. We used a minimal model cell, the alga Ostreococcus tauri, to uncover the role of potassium in linking these two cycles. We found direct reciprocal feedback between [K+]i and circadian gene expression. Inhibition of proliferation by manipulating potassium rhythms was dependent on the phase of the circadian cycle. Furthermore, we observed a total inhibition of cell proliferation when circadian gene expression is inhibited. Strikingly, under these conditions a sudden enforced gradient of extracellular potassium was sufficient to induce a round of cell division. Finally, we provide evidence that interactions between potassium and circadian rhythms also influence proliferation in mammalian cells. These results establish circadian regulation of intracellular potassium levels as a primary factor coupling the cell- and circadian cycles across diverse organisms.
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Affiliation(s)
- Sergio Gil Rodríguez
- School of Biological Sciences, University of Edinburgh, Max Born Crescent EH9 3BF Edinburgh, United Kingdom
| | - Priya Crosby
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Louise L. Hansen
- School of Biological Sciences, University of Edinburgh, Max Born Crescent EH9 3BF Edinburgh, United Kingdom
| | - Ellen Grünewald
- School of Biological Sciences, University of Edinburgh, Max Born Crescent EH9 3BF Edinburgh, United Kingdom
| | - Andrew D. Beale
- UKRI MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge, CB2 0QH, United Kingdom
| | - Rebecca K. Spangler
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Beverley M. Rabbitts
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Carrie L. Partch
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Alessandra Stangherlin
- Faculty of Medicine and University Hospital Cologne, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Institute for Mitochondrial Diseases and Ageing, University of Cologne, Joseph-Stelzmann-Str, 50931, Cologne, Germany
| | - John S. O’Neill
- UKRI MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge, CB2 0QH, United Kingdom
| | - Gerben van Ooijen
- School of Biological Sciences, University of Edinburgh, Max Born Crescent EH9 3BF Edinburgh, United Kingdom
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4
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Phanprasert Y, Maciszewski K, Gentekaki E, Dacks JB. Comparative genomic analysis illustrates evolutionary dynamics of multisubunit tethering complexes across green algal diversity. J Eukaryot Microbiol 2023; 70:e12935. [PMID: 35790054 DOI: 10.1111/jeu.12935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/21/2022] [Accepted: 06/29/2022] [Indexed: 01/13/2023]
Abstract
The chlorophyte algae are a dominant group of photosynthetic eukaryotes. Although many are photoautotrophs, there are also mixotrophs, heterotrophs, and even parasites. The physical characteristics of green algae are also highly diverse, varying greatly in size, shape, and habitat. Given this morphological and trophic diversity, we postulated that diversity may also exist in the protein components controlling intracellular movement of material by vesicular transport. One such set is the multisubunit tethering complexes (MTCs)-components regulating cargo delivery. As they span endomembrane organelles and are well-conserved across eukaryotes, MTCs should be a good proxy for assessing the evolutionary dynamics across the diversity of Chlorophyta. Our results reveal that while green algae carry a generally conserved and unduplicated complement of MTCs, some intriguing variation exists. Notably, we identified incomplete sets of TRAPPII, exocyst, and HOPS/CORVET components in all Mamiellophyceae, and what is more, not a single subunit of Dsl1 was found in Cymbomonas tetramitiformis. As the absence of Dsl1 has been correlated with having unusual peroxisomes, we searched for peroxisome biogenesis machinery, finding very few components in Cymbomonas, suggestive of peroxisome degeneration. Overall, we demonstrate conservation of MTCs across green algae, but with notable taxon-specific losses suggestive of unusual endomembrane systems.
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Affiliation(s)
| | - Kacper Maciszewski
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai, Thailand.,Gut Microbiome Research Group, Mae Fah Luang University, Chiang Rai, Thailand
| | - Joel B Dacks
- Division of Infectious Diseases, University of Alberta, Edmonton, Alberta, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.,Institute of Evolutionary Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
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5
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Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts. THE ISME JOURNAL 2021; 15:3129-3147. [PMID: 33972727 PMCID: PMC8528832 DOI: 10.1038/s41396-021-00989-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 03/08/2021] [Accepted: 04/14/2021] [Indexed: 02/03/2023]
Abstract
The marine picoeukaryote Bathycoccus prasinos has been considered a cosmopolitan alga, although recent studies indicate two ecotypes exist, Clade BI (B. prasinos) and Clade BII. Viruses that infect Bathycoccus Clade BI are known (BpVs), but not that infect BII. We isolated three dsDNA prasinoviruses from the Sargasso Sea against Clade BII isolate RCC716. The BII-Vs do not infect BI, and two (BII-V2 and BII-V3) have larger genomes (~210 kb) than BI-Viruses and BII-V1. BII-Vs share ~90% of their proteins, and between 65% to 83% of their proteins with sequenced BpVs. Phylogenomic reconstructions and PolB analyses establish close-relatedness of BII-V2 and BII-V3, yet BII-V2 has 10-fold higher infectivity and induces greater mortality on host isolate RCC716. BII-V1 is more distant, has a shorter latent period, and infects both available BII isolates, RCC716 and RCC715, while BII-V2 and BII-V3 do not exhibit productive infection of the latter in our experiments. Global metagenome analyses show Clade BI and BII algal relative abundances correlate positively with their respective viruses. The distributions delineate BI/BpVs as occupying lower temperature mesotrophic and coastal systems, whereas BII/BII-Vs occupy warmer temperature, higher salinity ecosystems. Accordingly, with molecular diagnostic support, we name Clade BII Bathycoccus calidus sp. nov. and propose that molecular diversity within this new species likely connects to the differentiated host-virus dynamics observed in our time course experiments. Overall, the tightly linked biogeography of Bathycoccus host and virus clades observed herein supports species-level host specificity, with strain-level variations in infection parameters.
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6
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Yusuf M, Farooq S, Robinson I, Lalani EN. Cryo-nanoscale chromosome imaging-future prospects. Biophys Rev 2020; 12:1257-1263. [PMID: 33006727 PMCID: PMC7575669 DOI: 10.1007/s12551-020-00757-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/04/2020] [Indexed: 01/30/2023] Open
Abstract
The high-order structure of mitotic chromosomes remains to be fully elucidated. How nucleosomes compact at various structural levels into a condensed mitotic chromosome is unclear. Cryogenic preservation and imaging have been applied for over three decades, keeping biological structures close to the native in vivo state. Despite being extensively utilized, this field is still wide open for mitotic chromosome research. In this review, we focus specifically on cryogenic efforts for determining the mitotic nanoscale chromatin structures. We describe vitrification methods, current status, and applications of advanced cryo-microscopy including future tools required for resolving the native architecture of these fascinating structures that hold the instructions to life.
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Affiliation(s)
- Mohammed Yusuf
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan.
| | - Safana Farooq
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan
| | - Ian Robinson
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
- Brookhaven National Lab, Upton, NY, 11973, USA
| | - El-Nasir Lalani
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan
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7
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Castillo YM, Sebastián M, Forn I, Grimsley N, Yau S, Moraru C, Vaqué D. Visualization of Viral Infection Dynamics in a Unicellular Eukaryote and Quantification of Viral Production Using Virus Fluorescence in situ Hybridization. Front Microbiol 2020; 11:1559. [PMID: 32765451 PMCID: PMC7379908 DOI: 10.3389/fmicb.2020.01559] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/16/2020] [Indexed: 11/13/2022] Open
Abstract
One of the major challenges in viral ecology is to assess the impact of viruses in controlling the abundance of specific hosts in the environment. To this end, techniques that enable the detection and quantification of virus-host interactions at the single-cell level are essential. With this goal in mind, we implemented virus fluorescence in situ hybridization (VirusFISH) using as a model the marine picoeukaryote Ostreococcus tauri and its virus Ostreococcus tauri virus 5 (OtV5). VirusFISH allowed the visualization and quantification of the proportion of infected cells during an infection cycle in experimental conditions. We were also able to quantify the abundance of free viruses released during cell lysis, discriminating OtV5 from other mid-level fluorescence phages in our non-axenic infected culture that were not easily distinguishable with flow cytometry. Our results showed that although the major lysis of the culture occurred between 24 and 48 h after OtV5 inoculation, some new viruses were already produced between 8 and 24 h. With this work, we demonstrate that VirusFISH is a promising technique to study specific virus-host interactions in non-axenic cultures and establish a framework for its application in complex natural communities.
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Affiliation(s)
- Yaiza M Castillo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain
| | - Marta Sebastián
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain.,Institute of Oceanography and Global Change (IOCAG), University of Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria, Spain
| | - Irene Forn
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain
| | - Nigel Grimsley
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanographic Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Sheree Yau
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain.,Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanographic Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Cristina Moraru
- Department of the Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain
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8
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Surviving Starvation: Proteomic and Lipidomic Profiling of Nutrient Deprivation in the Smallest Known Free-Living Eukaryote. Metabolites 2020; 10:metabo10070273. [PMID: 32635273 PMCID: PMC7407893 DOI: 10.3390/metabo10070273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/17/2020] [Accepted: 06/27/2020] [Indexed: 11/16/2022] Open
Abstract
Marine phytoplankton, comprising cyanobacteria, micro- and pico-algae are key to photosynthesis, oxygen production and carbon assimilation on Earth. The unicellular green picoalga Ostreococcus tauri holds a key position at the base of the green lineage of plants, which makes it an interesting model organism. O. tauri has adapted to survive in low levels of nitrogen and phosphorus in the open ocean and also during rapid changes in the levels of these nutrients in coastal waters. In this study, we have employed untargeted proteomic and lipidomic strategies to investigate the molecular responses of O. tauri to low-nitrogen and low-phosphorus environments. In the absence of external nitrogen, there was an elevation in the expression of ammonia and urea transporter proteins together with an accumulation of triglycerides. In phosphate-limiting conditions, the expression levels of phosphokinases and phosphate transporters were increased, indicating an attempt to maximise scavenging opportunities as opposed to energy conservation conditions. The production of betaine lipids was also elevated, highlighting a shift away from phospholipid metabolism. This finding was supported by the putative identification of betaine synthase in O. tauri. This work offers additional perspectives on the complex strategies that underpin the adaptive processes of the smallest known free-living eukaryote to alterations in environmental conditions.
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9
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Mullineaux PM, Exposito-Rodriguez M, Laissue PP, Smirnoff N, Park E. Spatial chloroplast-to-nucleus signalling involving plastid-nuclear complexes and stromules. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190405. [PMID: 32362250 PMCID: PMC7209948 DOI: 10.1098/rstb.2019.0405] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Communication between chloroplasts and the nucleus in response to various environmental cues may be mediated by various small molecules. Signalling specificity could be enhanced if the physical contact between these organelles facilitates direct transfer and prevents interference from other subcellular sources of the same molecules. Plant cells have plastid-nuclear complexes, which provide close physical contact between these organelles. Plastid-nuclear complexes have been proposed to facilitate transfer of photosynthesis-derived H2O2 to the nucleus in high light. Stromules (stroma filled tubular plastid extensions) may provide an additional conduit for transfer of a wider range of signalling molecules, including proteins. However, plastid-nuclear complexes and stromules have been hitherto treated as distinct phenomena. We suggest that plastid-nuclear complexes and stromules work in a coordinated manner so that, according to environmental conditions or developmental state, the two modes of connection contribute to varying extents. We hypothesize that this association is dynamic and that there may be a link between plastid-nuclear complexes and the development of stromules. Furthermore, the changes in contact could alter signalling specificity by allowing an extended or different range of signalling molecules to be delivered to the nucleus. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.
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Affiliation(s)
- Philip M Mullineaux
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | | | | | - Nicholas Smirnoff
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Eunsook Park
- Plant Immunity Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.,Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie WY 82071, USA
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10
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Ng CT, Gan L. Investigating eukaryotic cells with cryo-ET. Mol Biol Cell 2020; 31:87-100. [PMID: 31935172 PMCID: PMC6960407 DOI: 10.1091/mbc.e18-05-0329] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 01/06/2023] Open
Abstract
The interior of eukaryotic cells is mysterious. How do the large communities of macromolecular machines interact with each other? How do the structures and positions of these nanoscopic entities respond to new stimuli? Questions like these can now be answered with the help of a method called electron cryotomography (cryo-ET). Cryo-ET will ultimately reveal the inner workings of a cell at the protein, secondary structure, and perhaps even side-chain levels. Combined with genetic or pharmacological perturbation, cryo-ET will allow us to answer previously unimaginable questions, such as how structure, biochemistry, and forces are related in situ. Because it bridges structural biology and cell biology, cryo-ET is indispensable for structural cell biology-the study of the 3-D macromolecular structure of cells. Here we discuss some of the key ideas, strategies, auxiliary techniques, and innovations that an aspiring structural cell biologist will consider when planning to ask bold questions.
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Affiliation(s)
- Cai Tong Ng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
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11
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Mironov AA, Beznoussenko GV. Models of Intracellular Transport: Pros and Cons. Front Cell Dev Biol 2019; 7:146. [PMID: 31440506 PMCID: PMC6693330 DOI: 10.3389/fcell.2019.00146] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/16/2019] [Indexed: 12/22/2022] Open
Abstract
Intracellular transport is one of the most confusing issues in the field of cell biology. Many different models and their combinations have been proposed to explain the experimental data on intracellular transport. Here, we analyse the data related to the mechanisms of endoplasmic reticulum-to-Golgi and intra-Golgi transport from the point of view of the main models of intracellular transport; namely: the vesicular model, the diffusion model, the compartment maturation–progression model, and the kiss-and-run model. This review initially describes our current understanding of Golgi function, while highlighting the recent progress that has been made. It then continues to discuss the outstanding questions and potential avenues for future research with regard to the models of these transport steps. To compare the power of these models, we have applied the method proposed by K. Popper; namely, the formulation of prohibitive observations according to, and the consecutive evaluation of, previous data, on the basis on the new models. The levels to which the different models can explain the experimental observations are different, and to date, the most powerful has been the kiss-and-run model, whereas the least powerful has been the diffusion model.
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Affiliation(s)
- Alexander A Mironov
- Department of Cell Biology, The FIRC Institute of Molecular Oncology, Milan, Italy
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12
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Abstract
For automated acquisition of tilt series for electron tomography, software needs to handle complications such as movements of the sample in x/y and z, increased projected thickness at high tilt, specimen drift, etc. In addition, many applications require special functionality such as low dose acquisition, automated sequential (batch) tomography, or montage tomography. After reviewing how these difficulties can be addressed and a closer look at what advanced acquisition strategies are employed in biosciences, this chapter introduces acquisition software both developed in academia as well as by hardware vendors. It covers the hardware requirements and compatibility, the functional principle and workflow implemented, as well as what advanced functions are supported by the individual programs.
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Affiliation(s)
- Guenter P Resch
- Nexperion e.U.-Solutions for Electron Microscopy, Vienna, Austria.
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13
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Yokono M, Takabayashi A, Kishimoto J, Fujita T, Iwai M, Murakami A, Akimoto S, Tanaka A. The PSI-PSII Megacomplex in Green Plants. PLANT & CELL PHYSIOLOGY 2019; 60:1098-1108. [PMID: 30753722 DOI: 10.1093/pcp/pcz026] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 02/04/2019] [Indexed: 05/27/2023]
Abstract
Energy dissipation is crucial for land and shallow-water plants exposed to direct sunlight. Almost all green plants dissipate excess excitation energy to protect the photosystem reaction centers, photosystem II (PSII) and photosystem I (PSI), and continue to grow under strong light. In our previous work, we reported that about half of the photosystem reaction centers form a PSI-PSII megacomplex in Arabidopsis thaliana, and that the excess energy was transferred from PSII to PSI fast. However, the physiological function and structure of the megacomplex remained unclear. Here, we suggest that high-light adaptable sun-plants accumulate the PSI-PSII megacomplex more than shade-plants. In addition, PSI of sun-plants has a deep trap to receive excitation energy, which is low-energy chlorophylls showing fluorescence maxima longer than 730 nm. This deep trap may increase the high-light tolerance of PSI by improving excitation energy dissipation. Electron micrographs suggest that one PSII dimer is directly sandwiched between two PSIs with 2-fold rotational symmetry in the basic form of the PSI-PSII megacomplex in green plants. This structure should enable fast energy transfer from PSII to PSI and allow energy in PSII to be dissipated via the deep trap in PSI.
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Affiliation(s)
- Makio Yokono
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
- CREST, JST, Sapporo, Japan
- Nippon Flour Mills Co., Ltd., Innovation Center, Atsugi, Japan
| | - Atsushi Takabayashi
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
- CREST, JST, Sapporo, Japan
| | - Junko Kishimoto
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
- CREST, JST, Sapporo, Japan
| | - Tomomichi Fujita
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Masakazu Iwai
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Akio Murakami
- Kobe University Research Centre for Inland Seas, Awaji, Japan
- Graduate School of Science, Kobe University, Kobe, Japan
| | - Seiji Akimoto
- Graduate School of Science, Kobe University, Kobe, Japan
| | - Ayumi Tanaka
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
- CREST, JST, Sapporo, Japan
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14
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Feord HK, Dear FEG, Obbard DJ, van Ooijen G. A Magnesium Transport Protein Related to Mammalian SLC41 and Bacterial MgtE Contributes to Circadian Timekeeping in a Unicellular Green Alga. Genes (Basel) 2019; 10:genes10020158. [PMID: 30791470 PMCID: PMC6410215 DOI: 10.3390/genes10020158] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 01/29/2019] [Accepted: 02/12/2019] [Indexed: 11/16/2022] Open
Abstract
Circadian clocks in eukaryotes involve both transcriptional-translational feedback loops, post-translational regulation, and metabolic, non-transcriptional oscillations. We recently identified the involvement of circadian oscillations in the intracellular concentrations of magnesium ions (Mg2+i) that were conserved in three eukaryotic kingdoms. Mg2+i in turn contributes to transcriptional clock properties of period and amplitude, and can function as a zeitgeber to define phase. However, the mechanism-or mechanisms-responsible for the generation of Mg2+i oscillations, and whether these are functionally conserved across taxonomic groups, remain elusive. We employed the cellular clock model Ostreococcustauri to provide a first study of an MgtE domain-containing protein in the green lineage. OtMgtE shares homology with the mammalian SLC41A1 magnesium/sodium antiporter, which has previously been implicated in maintaining clock period. Using genetic overexpression, we found that OtMgtE contributes to both timekeeping and daily changes in Mg2+i. However, pharmacological experiments and protein sequence analyses indicated that critical differences exist between OtMgtE and either the ancestral MgtE channel or the mammalian SLC41 antiporters. We concluded that even though MgtE domain-containing proteins are only distantly related, these proteins retain a shared role in contributing to cellular timekeeping and the regulation of Mg2+i.
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Affiliation(s)
- Helen K Feord
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
| | - Frederick E G Dear
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
| | - Darren J Obbard
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
| | - Gerben van Ooijen
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
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15
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16
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Mironov AA, Dimov ID, Beznoussenko GV. Role of Intracellular Transport in the Centriole-Dependent Formation of Golgi Ribbon. Results Probl Cell Differ 2019; 67:49-79. [PMID: 31435792 DOI: 10.1007/978-3-030-23173-6_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The intracellular transport is the most confusing issue in the field of cell biology. The Golgi complex (GC) is the central station along the secretory pathway. It contains Golgi glycosylation enzymes, which are responsible for protein and lipid glycosylation, and in many cells, it is organized into a ribbon. Position and structure of the GC depend on the position and function of the centriole. Here, we analyze published data related to the role of centriole and intracellular transport (ICT) for the formation of Golgi ribbon and specifically stress the importance of the delivery of membranes containing cargo and membrane proteins to the cell centre where centriole/centrosome is localized. Additionally, we re-examined the formation of Golgi ribbon from the point of view of different models of ICT.
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Affiliation(s)
| | - Ivan D Dimov
- Department of Anatomy, Saint Petersburg State Paediatric Medical University, Saint Petersburg, Russia
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17
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Gerlitz M, Knopp M, Kapust N, Xavier JC, Martin WF. Elusive data underlying debate at the prokaryote-eukaryote divide. Biol Direct 2018; 13:21. [PMID: 31196150 PMCID: PMC6888934 DOI: 10.1186/s13062-018-0221-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 08/16/2018] [Indexed: 12/11/2022] Open
Abstract
Background The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenergetic membranes that they conferred to the common ancestor of all known eukaryotic lineages. A recent paper by Lynch and Marinov concluded that mitochondria were energetically irrelevant to eukaryote origin, a conclusion based on analyses of previously published numbers of various molecules and ribosomes per cell and cell volumes as a presumed proxy for the role of mitochondria in evolution. Their numbers were purportedly extracted from the literature. Results We have examined the numbers upon which the recent study was based. We report that for a sample of 80 numbers that were purportedly extracted from the literature and that underlie key inferences of the recent study, more than 50% of the values do not exist in the cited papers to which the numbers are attributed. The published result cannot be independently reproduced. Other numbers that the recent study reports differ inexplicably from those in the literature to which they are ascribed. We list the discrepancies between the recently published numbers and the purported literature sources of those numbers in a head to head manner so that the discrepancies are readily evident, although the source of error underlying the discrepancies remains obscure. Conclusion The data purportedly supporting the view that mitochondria had no impact upon eukaryotic evolution data exhibits notable irregularities. The paper in question evokes the impression that the published numbers are of up to seven significant digit accuracy, when in fact more than half the numbers are nowhere to be found in the literature to which they are attributed. Though the reasons for the discrepancies are unknown, it is important to air these issues, lest the prominent paper in question become a point source of a snowballing error through the literature or become interpreted as a form of evidence that mitochondria were irrelevant to eukaryote evolution. Reviewers This article was reviewed by Eric Bapteste, Jianzhi Zhang and Martin Lercher.
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Affiliation(s)
- Marie Gerlitz
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Michael Knopp
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Nils Kapust
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Joana C Xavier
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany.
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18
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Reipert S, Goldammer H, Richardson C, Goldberg MW, Hawkins TJ, Hollergschwandtner E, Kaufmann WA, Antreich S, Stierhof YD. Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution. J Histochem Cytochem 2018; 66:903-921. [PMID: 29969056 DOI: 10.1369/0022155418786698] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
For ultrafast fixation of biological samples to avoid artifacts, high-pressure freezing (HPF) followed by freeze substitution (FS) is preferred over chemical fixation at room temperature. After HPF, samples are maintained at low temperature during dehydration and fixation, while avoiding damaging recrystallization. This is a notoriously slow process. McDonald and Webb demonstrated, in 2011, that sample agitation during FS dramatically reduces the necessary time. Then, in 2015, we (H.G. and S.R.) introduced an agitation module into the cryochamber of an automated FS unit and demonstrated that the preparation of algae could be shortened from days to a couple of hours. We argued that variability in the processing, reproducibility, and safety issues are better addressed using automated FS units. For dissemination, we started low-cost manufacturing of agitation modules for two of the most widely used FS units, the Automatic Freeze Substitution Systems, AFS(1) and AFS2, from Leica Microsystems, using three dimensional (3D)-printing of the major components. To test them, several labs independently used the modules on a wide variety of specimens that had previously been processed by manual agitation, or without agitation. We demonstrate that automated processing with sample agitation saves time, increases flexibility with respect to sample requirements and protocols, and produces data of at least as good quality as other approaches.
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Affiliation(s)
- Siegfried Reipert
- Core Facility Cell Imaging and Ultrastructure Research, University of Vienna, Vienna, Austria
| | - Helmuth Goldammer
- Core Facility Cell Imaging and Ultrastructure Research, University of Vienna, Vienna, Austria
| | | | - Martin W Goldberg
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Timothy J Hawkins
- Department of Biosciences, Durham University, Durham, United Kingdom
| | | | - Walter A Kaufmann
- Electron Microscopy Facility, Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Sebastian Antreich
- Core Facility Cell Imaging and Ultrastructure Research, University of Vienna, Vienna, Austria
| | - York-Dieter Stierhof
- Center for Plant Molecular Biology (ZMBP), Microscopy, University of Tübingen, Tübingen, Germany
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19
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Cai S, Song Y, Chen C, Shi J, Gan L. Natural chromatin is heterogeneous and self-associates in vitro. Mol Biol Cell 2018; 29:1652-1663. [PMID: 29742050 PMCID: PMC6080658 DOI: 10.1091/mbc.e17-07-0449] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 04/10/2018] [Accepted: 05/04/2018] [Indexed: 11/23/2022] Open
Abstract
The 30-nm fiber is commonly formed by oligonucleosome arrays in vitro but rarely found inside cells. To determine how chromatin higher-order structure is controlled, we used electron cryotomography (cryo-ET) to study the undigested natural chromatin released from two single-celled organisms in which 30-nm fibers have not been observed in vivo: picoplankton and yeast. In the presence of divalent cations, most of the chromatin from both organisms is condensed into a large mass in vitro. Rare irregular 30-nm fibers, some of which include face-to-face nucleosome interactions, do form at the periphery of this mass. In the absence of divalent cations, picoplankton chromatin decondenses into open zigzags. By contrast, yeast chromatin mostly remains condensed, with very few open motifs. Yeast chromatin packing is largely unchanged in the absence of linker histone and mildly decondensed when histones are more acetylated. Natural chromatin is therefore generally nonpermissive of regular motifs, even at the level of oligonucleosomes.
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Affiliation(s)
- Shujun Cai
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Yajiao Song
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Chen Chen
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Jian Shi
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
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20
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Abstract
Trypanosoma brucei is a highly invasive pathogen capable of penetrating deeply into host tissues. To understand how flagellar motility facilitates cell penetration, we used cryo-electron tomography (cryo-ET) to visualize two genetically anucleate mutants with different flagellar motility behaviors. We found that the T. brucei cell body is highly deformable as defined by changes in cytoskeletal twist and spacing, in response to flagellar beating and environmental conditions. Based on the cryo-ET models, we proposed a mechanism of how flagellum motility is coupled to cell shape changes, which may facilitate penetration through size-limiting barriers. In the unicellular parasite Trypanosoma brucei, the causative agent of human African sleeping sickness, complex swimming behavior is driven by a flagellum laterally attached to the long and slender cell body. Using microfluidic assays, we demonstrated that T. brucei can penetrate through an orifice smaller than its maximum diameter. Efficient motility and penetration depend on active flagellar beating. To understand how active beating of the flagellum affects the cell body, we genetically engineered T. brucei to produce anucleate cytoplasts (zoids and minis) with different flagellar attachment configurations and different swimming behaviors. We used cryo-electron tomography (cryo-ET) to visualize zoids and minis vitrified in different motility states. We showed that flagellar wave patterns reflective of their motility states are coupled to cytoskeleton deformation. Based on these observations, we propose a mechanism for how flagellum beating can deform the cell body via a flexible connection between the flagellar axoneme and the cell body. This mechanism may be critical for T. brucei to disseminate in its host through size-limiting barriers.
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21
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Moser TH, Mehta H, Park C, Kelly RT, Shokuhfar T, Evans JE. The role of electron irradiation history in liquid cell transmission electron microscopy. SCIENCE ADVANCES 2018; 4:eaaq1202. [PMID: 29725619 PMCID: PMC5930397 DOI: 10.1126/sciadv.aaq1202] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 03/13/2018] [Indexed: 05/25/2023]
Abstract
In situ liquid cell transmission electron microscopy (LC-TEM) allows dynamic nanoscale characterization of systems in a hydrated state. Although powerful, this technique remains impaired by issues of repeatability that limit experimental fidelity and hinder the identification and control of some variables underlying observed dynamics. We detail new LC-TEM devices that improve experimental reproducibility by expanding available imaging area and providing a platform for investigating electron flux history on the sample. Irradiation history is an important factor influencing LC-TEM results that has, to this point, been largely qualitatively and not quantitatively described. We use these devices to highlight the role of cumulative electron flux history on samples from both nanoparticle growth and biological imaging experiments and demonstrate capture of time zero, low-dose images on beam-sensitive samples. In particular, the ability to capture pristine images of biological samples, where the acquired image is the first time that the cell experiences significant electron flux, allowed us to determine that nanoparticle movement compared to the cell membrane was a function of cell damage and therefore an artifact rather than visualizing cell dynamics in action. These results highlight just a subset of the new science that is accessible with LC-TEM through the new multiwindow devices with patterned focusing aides.
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Affiliation(s)
- Trevor H. Moser
- Environmental Molecular Sciences Laboratory, 3335 Innovation Boulevard, Richland, WA 99354, USA
- Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Hardeep Mehta
- Environmental Molecular Sciences Laboratory, 3335 Innovation Boulevard, Richland, WA 99354, USA
| | - Chiwoo Park
- Florida State University, 600 West College Avenue, Tallahassee, FL 32306, USA
| | - Ryan T. Kelly
- Environmental Molecular Sciences Laboratory, 3335 Innovation Boulevard, Richland, WA 99354, USA
| | - Tolou Shokuhfar
- Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
- University of Illinois Chicago, 1200 West Harrison Street, Chicago, IL 60607, USA
| | - James E. Evans
- Environmental Molecular Sciences Laboratory, 3335 Innovation Boulevard, Richland, WA 99354, USA
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
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22
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Cyrklaff M, Frischknecht F, Kudryashev M. Functional insights into pathogen biology from 3D electron microscopy. FEMS Microbiol Rev 2018; 41:828-853. [PMID: 28962014 DOI: 10.1093/femsre/fux041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 07/25/2017] [Indexed: 01/10/2023] Open
Abstract
In recent years, novel imaging approaches revolutionised our understanding of the cellular and molecular biology of microorganisms. These include advances in fluorescent probes, dynamic live cell imaging, superresolution light and electron microscopy. Currently, a major transition in the experimental approach shifts electron microscopy studies from a complementary technique to a method of choice for structural and functional analysis. Here we review functional insights into the molecular architecture of viruses, bacteria and parasites as well as interactions with their respective host cells gained from studies using cryogenic electron tomography and related methodologies.
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Affiliation(s)
- Marek Cyrklaff
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Mikhail Kudryashev
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt, Max-von-Laue Strasse 17, 60438 Frankfurt, Germany
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23
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Popp D, Koh F, Scipion CPM, Ghoshdastider U, Narita A, Holmes KC, Robinson RC. Advances in Structural Biology and the Application to Biological Filament Systems. Bioessays 2018; 40:e1700213. [PMID: 29484695 DOI: 10.1002/bies.201700213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/10/2018] [Indexed: 11/10/2022]
Abstract
Structural biology has experienced several transformative technological advances in recent years. These include: development of extremely bright X-ray sources (microfocus synchrotron beamlines and free electron lasers) and the use of electrons to extend protein crystallography to ever decreasing crystal sizes; and an increase in the resolution attainable by cryo-electron microscopy. Here we discuss the use of these techniques in general terms and highlight their application for biological filament systems, an area that is severely underrepresented in atomic resolution structures. We assemble a model of a capped tropomyosin-actin minifilament to demonstrate the utility of combining structures determined by different techniques. Finally, we survey the methods that attempt to transform high resolution structural biology into more physiological environments, such as the cell. Together these techniques promise a compelling decade for structural biology and, more importantly, they will provide exciting discoveries in understanding the designs and purposes of biological machines.
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Affiliation(s)
- David Popp
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore
| | - Fujiet Koh
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore
| | - Clement P M Scipion
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore.,Department of Biochemistry Yong Loo Lin School of Medicine National University of Singapore, Singapore 117597, Singapore
| | - Umesh Ghoshdastider
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore
| | - Akihiro Narita
- Nagoya University Graduate School of Science Structural Biology Research Center and Division of Biological Sciences, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Kenneth C Holmes
- Max Planck Institute for Medical Research, D69120 Heidelberg, Germany
| | - Robert C Robinson
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore.,Department of Biochemistry Yong Loo Lin School of Medicine National University of Singapore, Singapore 117597, Singapore.,Research Institute for Interdisciplinary Science Okayama University, Okayama 700-8530, Japan
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24
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Limardo AJ, Sudek S, Choi CJ, Poirier C, Rii YM, Blum M, Roth R, Goodenough U, Church MJ, Worden AZ. Quantitative biogeography of picoprasinophytes establishes ecotype distributions and significant contributions to marine phytoplankton. Environ Microbiol 2017; 19:3219-3234. [PMID: 28585420 DOI: 10.1111/1462-2920.13812] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/26/2017] [Accepted: 05/30/2017] [Indexed: 12/17/2022]
Abstract
Bathycoccus and Ostreococcus are broadly distributed marine picoprasinophyte algae. We enumerated small phytoplankton using flow cytometry and qPCR assays for phylogenetically distinct Bathycoccus clades BI and BII and Ostreococcus clades OI and OII. Among 259 photic-zone samples from transects and time-series, Ostreococcus maxima occurred in the North Pacific coastal upwelling for OI (36 713 ± 1485 copies ml-1 ) and the Kuroshio Front for OII (50 189 ± 561 copies ml-1 ) and the two overlapped only in frontal regions. The Bathycoccus overlapped more often with maxima along Line-P for BI (10 667 ± 1299 copies ml-1 ) and the tropical Atlantic for BII (4125 ± 339 copies ml-1 ). Only BII and OII were detected at warm oligotrophic sites, accounting for 34 ± 13% of 1589 ± 448 eukaryotic phytoplankton cells ml-1 (annual average) at Station ALOHA's deep chlorophyll maximum. Significant distributional and molecular differences lead us to propose that Bathycoccus clade BII represents a separate species which tolerates higher temperature oceanic conditions than Bathycoccus prasinos (BI). Morphological differences were not evident, but quick-freeze deep-etch electron microscopy provided insight into Bathycoccus scale formation. Our results highlight the importance of quantitative seasonal abundance data for inferring ecological distributions and demonstrate significant, differential picoprasinophyte contributions in mesotrophic and open-ocean waters.
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Affiliation(s)
- Alexander J Limardo
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,University of California Santa Cruz, Santa Cruz, CA, USA
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Chang Jae Choi
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Camille Poirier
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | | | - Marguerite Blum
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Robyn Roth
- Washington University School of Medicine, St. Louis, MO, USA
| | | | | | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,University of California Santa Cruz, Santa Cruz, CA, USA
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25
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Degraeve-Guilbault C, Bréhélin C, Haslam R, Sayanova O, Marie-Luce G, Jouhet J, Corellou F. Glycerolipid Characterization and Nutrient Deprivation-Associated Changes in the Green Picoalga Ostreococcus tauri. PLANT PHYSIOLOGY 2017; 173:2060-2080. [PMID: 28235892 PMCID: PMC5373045 DOI: 10.1104/pp.16.01467] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 02/23/2017] [Indexed: 05/23/2023]
Abstract
The picoalga Ostreococcus tauri is a minimal photosynthetic eukaryote that has been used as a model system. O. tauri is known to efficiently produce docosahexaenoic acid (DHA). We provide a comprehensive study of the glycerolipidome of O. tauri and validate this species as model for related picoeukaryotes. O. tauri lipids displayed unique features that combined traits from the green and the chromalveolate lineages. The betaine lipid diacylglyceryl-hydroxymethyl-trimethyl-β-alanine and phosphatidyldimethylpropanethiol, both hallmarks of chromalveolates, were identified as presumed extraplastidial lipids. DHA was confined to these lipids, while plastidial lipids of prokaryotic type were characterized by the overwhelming presence of ω-3 C18 polyunsaturated fatty acids (FAs), 18:5 being restricted to galactolipids. C16:4, an FA typical of green microalgae galactolipids, also was a major component of O. tauri extraplastidial lipids, while the 16:4-coenzyme A (CoA) species was not detected. Triacylglycerols (TAGs) displayed the complete panel of FAs, and many species exhibited combinations of FAs diagnostic for plastidial and extraplastidial lipids. Importantly, under nutrient deprivation, 16:4 and ω-3 C18 polyunsaturated FAs accumulated into de novo synthesized TAGs while DHA-TAG species remained rather stable, indicating an increased contribution of FAs of plastidial origin to TAG synthesis. Nutrient deprivation further severely down-regulated the conversion of 18:3 to 18:4, resulting in obvious inversion of the 18:3/18:4 ratio in plastidial lipids, TAGs, as well as acyl-CoAs. The fine-tuned and dynamic regulation of the 18:3/18:4 ratio suggested an important physiological role of these FAs in photosynthetic membranes. Acyl position in structural and storage lipids together with acyl-CoA analysis further help to determine mechanisms possibly involved in glycerolipid synthesis.
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Affiliation(s)
- Charlotte Degraeve-Guilbault
- Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Centre National de la Recherche Scientifique, Université de Bordeaux BP81, F-33882 Villenave D'Ornon, France (C.D.-G., C.B., G.M.-L., F.C.)
- Rothamsted Research, Biological, Chemistry, Harpenden AL5 2JQ, United Kingdom (R.H., O.S.); and
- Laboratoire de Biologie Cellulaire et Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, BIG, Commissariat à l'Energie Atomique-Grenoble, 38054 Grenoble cedex 9, France (J.J.)
| | - Claire Bréhélin
- Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Centre National de la Recherche Scientifique, Université de Bordeaux BP81, F-33882 Villenave D'Ornon, France (C.D.-G., C.B., G.M.-L., F.C.)
- Rothamsted Research, Biological, Chemistry, Harpenden AL5 2JQ, United Kingdom (R.H., O.S.); and
- Laboratoire de Biologie Cellulaire et Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, BIG, Commissariat à l'Energie Atomique-Grenoble, 38054 Grenoble cedex 9, France (J.J.)
| | - Richard Haslam
- Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Centre National de la Recherche Scientifique, Université de Bordeaux BP81, F-33882 Villenave D'Ornon, France (C.D.-G., C.B., G.M.-L., F.C.)
- Rothamsted Research, Biological, Chemistry, Harpenden AL5 2JQ, United Kingdom (R.H., O.S.); and
- Laboratoire de Biologie Cellulaire et Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, BIG, Commissariat à l'Energie Atomique-Grenoble, 38054 Grenoble cedex 9, France (J.J.)
| | - Olga Sayanova
- Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Centre National de la Recherche Scientifique, Université de Bordeaux BP81, F-33882 Villenave D'Ornon, France (C.D.-G., C.B., G.M.-L., F.C.)
- Rothamsted Research, Biological, Chemistry, Harpenden AL5 2JQ, United Kingdom (R.H., O.S.); and
- Laboratoire de Biologie Cellulaire et Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, BIG, Commissariat à l'Energie Atomique-Grenoble, 38054 Grenoble cedex 9, France (J.J.)
| | - Glawdys Marie-Luce
- Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Centre National de la Recherche Scientifique, Université de Bordeaux BP81, F-33882 Villenave D'Ornon, France (C.D.-G., C.B., G.M.-L., F.C.)
- Rothamsted Research, Biological, Chemistry, Harpenden AL5 2JQ, United Kingdom (R.H., O.S.); and
- Laboratoire de Biologie Cellulaire et Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, BIG, Commissariat à l'Energie Atomique-Grenoble, 38054 Grenoble cedex 9, France (J.J.)
| | - Juliette Jouhet
- Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Centre National de la Recherche Scientifique, Université de Bordeaux BP81, F-33882 Villenave D'Ornon, France (C.D.-G., C.B., G.M.-L., F.C.)
- Rothamsted Research, Biological, Chemistry, Harpenden AL5 2JQ, United Kingdom (R.H., O.S.); and
- Laboratoire de Biologie Cellulaire et Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, BIG, Commissariat à l'Energie Atomique-Grenoble, 38054 Grenoble cedex 9, France (J.J.)
| | - Florence Corellou
- Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Centre National de la Recherche Scientifique, Université de Bordeaux BP81, F-33882 Villenave D'Ornon, France (C.D.-G., C.B., G.M.-L., F.C.);
- Rothamsted Research, Biological, Chemistry, Harpenden AL5 2JQ, United Kingdom (R.H., O.S.); and
- Laboratoire de Biologie Cellulaire et Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, BIG, Commissariat à l'Energie Atomique-Grenoble, 38054 Grenoble cedex 9, France (J.J.)
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Different Golgi ultrastructure across species and tissues: Implications under functional and pathological conditions, and an attempt at classification. Tissue Cell 2017; 49:186-201. [DOI: 10.1016/j.tice.2016.12.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 12/05/2016] [Accepted: 12/05/2016] [Indexed: 02/08/2023]
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Lynch M, Marinov GK. Membranes, energetics, and evolution across the prokaryote-eukaryote divide. eLife 2017; 6:20437. [PMID: 28300533 PMCID: PMC5354521 DOI: 10.7554/elife.20437] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 01/17/2017] [Indexed: 12/19/2022] Open
Abstract
The evolution of the eukaryotic cell marked a profound moment in Earth’s history, with most of the visible biota coming to rely on intracellular membrane-bound organelles. It has been suggested that this evolutionary transition was critically dependent on the movement of ATP synthesis from the cell surface to mitochondrial membranes and the resultant boost to the energetic capacity of eukaryotic cells. However, contrary to this hypothesis, numerous lines of evidence suggest that eukaryotes are no more bioenergetically efficient than prokaryotes. Thus, although the origin of the mitochondrion was a key event in evolutionary history, there is no reason to think membrane bioenergetics played a direct, causal role in the transition from prokaryotes to eukaryotes and the subsequent explosive diversification of cellular and organismal complexity. Over time, life on Earth has evolved into three large groups: archaea, bacteria, and eukaryotes. The most familiar forms of life – such as fungi, plants and animals – all belong to the eukaryotes. Bacteria and archaea are simpler, single-celled organisms and are collectively referred to as prokaryotes. The hallmark feature that distinguishes eukaryotes from prokaryotes is that eukaryotic cells contain compartments called organelles that are surrounded by membranes. Each organelle supports different activities in the cell. Mitochondria, for example, are organelles that provide eukaryotes with most of their energy by producing energy-rich molecules called ATP. Prokaryotes lack mitochondria and instead produce their ATP on their cell surface membrane. Some researchers have suggested that mitochondria might actually be one of the reasons that eukaryotic cells are typically larger than prokaryotes and more varied in their shape and structure. The thinking is that producing ATP on dedicated membranes inside the cell, rather than on the cell surface, boosted the amount of energy available to eukaryotic cells and allowed them to diversify more. However, other researchers are not convinced by this view. Moreover, some recent evidence suggested that eukaryotes are no more efficient in producing energy than prokaryotes. Lynch and Marinov have now used computational and comparative analysis to compare the energy efficiency of different organisms including prokaryotes and eukaryotes grown under defined conditions. To do the comparison, the results were scaled based on cell volume and the total surface area deployed in energy production. From their findings, Lynch and Marinov concluded that mitochondria did not enhance how much energy eukaryotes could produce per unit of cell volume in any substantial way. Although the origin of mitochondria was certainly a key event in evolutionary history, it is unlikely to have been responsible for the diversity and complexity of today’s life forms.
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Affiliation(s)
- Michael Lynch
- Department of Biology, Indiana University, Bloomington, United States
| | - Georgi K Marinov
- Department of Biology, Indiana University, Bloomington, United States
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Field Guide to Plant Model Systems. Cell 2017; 167:325-339. [PMID: 27716506 DOI: 10.1016/j.cell.2016.08.031] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/28/2016] [Accepted: 08/15/2016] [Indexed: 12/20/2022]
Abstract
For the past several decades, advances in plant development, physiology, cell biology, and genetics have relied heavily on the model (or reference) plant Arabidopsis thaliana. Arabidopsis resembles other plants, including crop plants, in many but by no means all respects. Study of Arabidopsis alone provides little information on the evolutionary history of plants, evolutionary differences between species, plants that survive in different environments, or plants that access nutrients and photosynthesize differently. Empowered by the availability of large-scale sequencing and new technologies for investigating gene function, many new plant models are being proposed and studied.
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de los Reyes P, Romero-Campero FJ, Ruiz MT, Romero JM, Valverde F. Evolution of Daily Gene Co-expression Patterns from Algae to Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1217. [PMID: 28751903 PMCID: PMC5508029 DOI: 10.3389/fpls.2017.01217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 06/28/2017] [Indexed: 05/04/2023]
Abstract
Daily rhythms play a key role in transcriptome regulation in plants and microalgae orchestrating responses that, among other processes, anticipate light transitions that are essential for their metabolism and development. The recent accumulation of genome-wide transcriptomic data generated under alternating light:dark periods from plants and microalgae has made possible integrative and comparative analysis that could contribute to shed light on the evolution of daily rhythms in the green lineage. In this work, RNA-seq and microarray data generated over 24 h periods in different light regimes from the eudicot Arabidopsis thaliana and the microalgae Chlamydomonas reinhardtii and Ostreococcus tauri have been integrated and analyzed using gene co-expression networks. This analysis revealed a reduction in the size of the daily rhythmic transcriptome from around 90% in Ostreococcus, being heavily influenced by light transitions, to around 40% in Arabidopsis, where a certain independence from light transitions can be observed. A novel Multiple Bidirectional Best Hit (MBBH) algorithm was applied to associate single genes with a family of potential orthologues from evolutionary distant species. Gene duplication, amplification and divergence of rhythmic expression profiles seems to have played a central role in the evolution of gene families in the green lineage such as Pseudo Response Regulators (PRRs), CONSTANS-Likes (COLs), and DNA-binding with One Finger (DOFs). Gene clustering and functional enrichment have been used to identify groups of genes with similar rhythmic gene expression patterns. The comparison of gene clusters between species based on potential orthologous relationships has unveiled a low to moderate level of conservation of daily rhythmic expression patterns. However, a strikingly high conservation was found for the gene clusters exhibiting their highest and/or lowest expression value during the light transitions.
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Affiliation(s)
- Pedro de los Reyes
- Plant Development Unit, Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de SevillaSeville, Spain
| | - Francisco J. Romero-Campero
- Plant Development Unit, Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de SevillaSeville, Spain
- Department of Computer Science and Artificial Intelligence, Universidad de SevillaSeville, Spain
| | - M. Teresa Ruiz
- Plant Development Unit, Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de SevillaSeville, Spain
| | - José M. Romero
- Plant Development Unit, Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de SevillaSeville, Spain
| | - Federico Valverde
- Plant Development Unit, Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de SevillaSeville, Spain
- *Correspondence: Federico Valverde
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Hirth M, Liverani S, Mahlow S, Bouget FY, Pohnert G, Sasso S. Metabolic profiling identifies trehalose as an abundant and diurnally fluctuating metabolite in the microalga Ostreococcus tauri. Metabolomics 2017; 13:68. [PMID: 28473745 PMCID: PMC5392535 DOI: 10.1007/s11306-017-1203-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/31/2017] [Indexed: 12/18/2022]
Abstract
INTRODUCTION The picoeukaryotic alga Ostreococcus tauri (Chlorophyta) belongs to the widespread group of marine prasinophytes. Despite its ecological importance, little is known about the metabolism of this alga. OBJECTIVES In this work, changes in the metabolome were quantified when O. tauri was grown under alternating cycles of 12 h light and 12 h darkness. METHODS Algal metabolism was analyzed by gas chromatography-mass spectrometry. Using fluorescence-activated cell sorting, the bacteria associated with O. tauri were depleted to below 0.1% of total cells at the time of metabolic profiling. RESULTS Of 111 metabolites quantified over light-dark cycles, 20 (18%) showed clear diurnal variations. The strongest fluctuations were found for trehalose. With an intracellular concentration of 1.6 mM in the dark, this disaccharide was six times more abundant at night than during the day. This fluctuation pattern of trehalose may be a consequence of starch degradation or of the synchronized cell cycle. On the other hand, maltose (and also sucrose) was below the detection limit (~10 μM). Accumulation of glycine in the light is in agreement with the presence of a classical glycolate pathway of photorespiration. We also provide evidence for the presence of fatty acid methyl and ethyl esters in O. tauri. CONCLUSIONS This study shows how the metabolism of O. tauri adapts to day and night and gives new insights into the configuration of the carbon metabolism. In addition, several less common metabolites were identified.
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Affiliation(s)
- Matthias Hirth
- 0000 0001 1939 2794grid.9613.dInstitute of General Botany and Plant Physiology, Friedrich Schiller University, Jena, Germany
| | - Silvia Liverani
- 0000 0001 0724 6933grid.7728.aDepartment of Mathematics, Brunel University London, Uxbridge, UK
| | - Sebastian Mahlow
- 0000 0001 1939 2794grid.9613.dInstitute of General Botany and Plant Physiology, Friedrich Schiller University, Jena, Germany
| | - François-Yves Bouget
- 0000 0001 2369 4306grid.463752.1Sorbonne Universités, UPMC Univ Paris 06 & Centre National pour la Recherche Scientifique CNRS, UMR 7621, Laboratoire d’Océanographie Microbienne, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Georg Pohnert
- 0000 0001 1939 2794grid.9613.dInstitute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- 0000 0004 0491 7131grid.418160.aMax Planck Institute for Chemical Ecology, Jena, Germany
| | - Severin Sasso
- 0000 0001 1939 2794grid.9613.dInstitute of General Botany and Plant Physiology, Friedrich Schiller University, Jena, Germany
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Kollmar M. Fine-Tuning Motile Cilia and Flagella: Evolution of the Dynein Motor Proteins from Plants to Humans at High Resolution. Mol Biol Evol 2016; 33:3249-3267. [PMID: 27880711 PMCID: PMC5100056 DOI: 10.1093/molbev/msw213] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The flagellum is a key innovation linked to eukaryogenesis. It provides motility by regulated cycles of bending and bend propagation, which are thought to be controlled by a complex arrangement of seven distinct dyneins in repeated patterns of outer- (OAD) and inner-arm dynein (IAD) complexes. Electron tomography showed high similarity of this axonemal repeat pattern across ciliates, algae, and animals, but the diversity of dynein sequences across the eukaryotes has not yet comprehensively been resolved and correlated with structural data. To shed light on the evolution of the axoneme I performed an exhaustive analysis of dyneins using the available sequenced genome data. Evidence from motor domain phylogeny allowed expanding the current set of nine dynein subtypes by eight additional isoforms with, however, restricted taxonomic distributions. I confirmed the presence of the nine dyneins in all eukaryotic super-groups indicating their origin predating the last eukaryotic common ancestor. The comparison of the N-terminal tail domains revealed a most likely axonemal dynein origin of the new classes, a group of chimeric dyneins in plants/algae and Stramenopiles, and the unique domain architecture and origin of the outermost OADs present in green algae and ciliates but not animals. The correlation of sequence and structural data suggests the single-headed class-8 and class-9 dyneins to localize to the distal end of the axonemal repeat and the class-7 dyneins filling the region up to the proximal heterodimeric IAD. Tracing dynein gene duplications across the eukaryotes indicated ongoing diversification and fine-tuning of flagellar functions in extant taxa and species.
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Affiliation(s)
- Martin Kollmar
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany
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Robinson DG, Neuhaus JM. Receptor-mediated sorting of soluble vacuolar proteins: myths, facts, and a new model. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4435-49. [PMID: 27262127 DOI: 10.1093/jxb/erw222] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
To prevent their being released to the cell exterior, acid hydrolases are recognized by receptors at some point in the secretory pathway and diverted towards the lytic compartment of the cell (lysosome or vacuole). In animal cells, the receptor is called the mannosyl 6-phosphate receptor (MPR) and it binds hydrolase ligands in the trans-Golgi network (TGN). These ligands are then sequestered into clathrin-coated vesicles (CCVs) because of motifs in the cytosolic tail of the MPR which interact first with monomeric adaptors (Golgi-localized, Gamma-ear-containing, ARF-binding proteins, GGAs) and then with tetrameric (adaptin) adaptor complexes. The CCVs then fuse with an early endosome, whose more acidic lumen causes the ligands to dissociate. The MPRs are then recycled back to the TGN via retromer-coated carriers. Plants have vacuolar sorting receptors (VSRs) which were originally identified in CCVs isolated from pea (Pisum sativum L.) cotyledons. It was therefore assumed that VSRs would have an analogous function in plants to MPRs in animals. Although this dogma has enjoyed wide support over the last 20 years there are many inconsistencies. Recently, results have been published which are quite contrary to it. It now emerges that VSRs and their ligands can interact very early in the secretory pathway, and dissociate in the TGN, which, in contrast to its mammalian counterpart, has a pH of 5.5. Multivesicular endosomes in plants lack proton pump complexes and consequently have an almost neutral internal pH, which discounts them as organelles of pH-dependent receptor-ligand dissociation. These data force a critical re-evaluation of the role of CCVs at the TGN, especially considering that vacuolar cargo ligands have never been identified in them. We propose that one population of TGN-derived CCVs participate in retrograde transport of VSRs from the TGN. We also present a new model to explain how secretory and vacuolar cargo proteins are effectively separated after entering the late Golgi/TGN compartments.
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Affiliation(s)
- David G Robinson
- Centre for Organismal Studies (COS), University of Heidelberg, Germany
| | - Jean-Marc Neuhaus
- Institute of Biology, Laboratory of Cell and Molecular Biology, University of Neuchatel, Switzerland
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Lelandais G, Scheiber I, Paz-Yepes J, Lozano JC, Botebol H, Pilátová J, Žárský V, Léger T, Blaiseau PL, Bowler C, Bouget FY, Camadro JM, Sutak R, Lesuisse E. Ostreococcus tauri is a new model green alga for studying iron metabolism in eukaryotic phytoplankton. BMC Genomics 2016; 17:319. [PMID: 27142620 PMCID: PMC4855317 DOI: 10.1186/s12864-016-2666-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/26/2016] [Indexed: 11/17/2022] Open
Abstract
Background Low iron bioavailability is a common feature of ocean surface water and therefore micro-algae developed original strategies to optimize iron uptake and metabolism. The marine picoeukaryotic green alga Ostreococcus tauri is a very good model for studying physiological and genetic aspects of the adaptation of the green algal lineage to the marine environment: it has a very compact genome, is easy to culture in laboratory conditions, and can be genetically manipulated by efficient homologous recombination. In this study, we aimed at characterizing the mechanisms of iron assimilation in O. tauri by combining genetics and physiological tools. Specifically, we wanted to identify and functionally characterize groups of genes displaying tightly orchestrated temporal expression patterns following the exposure of cells to iron deprivation and day/night cycles, and to highlight unique features of iron metabolism in O. tauri, as compared to the freshwater model alga Chalamydomonas reinhardtii. Results We used RNA sequencing to investigated the transcriptional responses to iron limitation in O. tauri and found that most of the genes involved in iron uptake and metabolism in O. tauri are regulated by day/night cycles, regardless of iron status. O. tauri lacks the classical components of a reductive iron uptake system, and has no obvious iron regulon. Iron uptake appears to be copper-independent, but is regulated by zinc. Conversely, iron deprivation resulted in the transcriptional activation of numerous genes encoding zinc-containing regulation factors. Iron uptake is likely mediated by a ZIP-family protein (Ot-Irt1) and by a new Fea1-related protein (Ot-Fea1) containing duplicated Fea1 domains. The adaptation of cells to iron limitation involved an iron-sparing response tightly coordinated with diurnal cycles to optimize cell functions and synchronize these functions with the day/night redistribution of iron orchestrated by ferritin, and a stress response based on the induction of thioredoxin-like proteins, of peroxiredoxin and of tesmin-like methallothionein rather than ascorbate. We briefly surveyed the metabolic remodeling resulting from iron deprivation. Conclusions The mechanisms of iron uptake and utilization by O. tauri differ fundamentally from those described in C. reinhardtii. We propose this species as a new model for investigation of iron metabolism in marine microalgae. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2666-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gaëlle Lelandais
- CNRS, Institut Jacques Monod, Université Paris Diderot-Paris 7, F-75013, Paris, France
| | - Ivo Scheiber
- Department of Parasitology, Faculty of Science, Charles University in Prague, 12844, Prague, Czech Republic
| | - Javier Paz-Yepes
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Jean-Claude Lozano
- Sorbonne Universités, University Pierre et Marie Curie, University of Paris VI, CNRS, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Hugo Botebol
- Sorbonne Universités, University Pierre et Marie Curie, University of Paris VI, CNRS, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Jana Pilátová
- Department of Parasitology, Faculty of Science, Charles University in Prague, 12844, Prague, Czech Republic
| | - Vojtěch Žárský
- Department of Parasitology, Faculty of Science, Charles University in Prague, 12844, Prague, Czech Republic
| | - Thibaut Léger
- CNRS, Institut Jacques Monod, Université Paris Diderot-Paris 7, F-75013, Paris, France
| | - Pierre-Louis Blaiseau
- Sorbonne Universités, University Pierre et Marie Curie, University of Paris VI, CNRS, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Chris Bowler
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - François-Yves Bouget
- Sorbonne Universités, University Pierre et Marie Curie, University of Paris VI, CNRS, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Jean-Michel Camadro
- CNRS, Institut Jacques Monod, Université Paris Diderot-Paris 7, F-75013, Paris, France
| | - Robert Sutak
- Department of Parasitology, Faculty of Science, Charles University in Prague, 12844, Prague, Czech Republic.
| | - Emmanuel Lesuisse
- CNRS, Institut Jacques Monod, Université Paris Diderot-Paris 7, F-75013, Paris, France.
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Reply to Lane and Martin: Mitochondria do not boost the bioenergetic capacity of eukaryotic cells. Proc Natl Acad Sci U S A 2016; 113:E667-8. [PMID: 26811483 DOI: 10.1073/pnas.1523394113] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Irobalieva RN, Martins B, Medalia O. Cellular structural biology as revealed by cryo-electron tomography. J Cell Sci 2016; 129:469-76. [DOI: 10.1242/jcs.171967] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
ABSTRACT
Understanding the function of cellular machines requires a thorough analysis of the structural elements that underline their function. Electron microscopy (EM) has been pivotal in providing information about cellular ultrastructure, as well as macromolecular organization. Biological materials can be physically fixed by vitrification and imaged with cryo-electron tomography (cryo-ET) in a close-to-native condition. Using this technique, one can acquire three-dimensional (3D) information about the macromolecular architecture of cells, depict unique cellular states and reconstruct molecular networks. Technical advances over the last few years, such as improved sample preparation and electron detection methods, have been instrumental in obtaining data with unprecedented structural details. This presents an exciting opportunity to explore the molecular architecture of both individual cells and multicellular organisms at nanometer to subnanometer resolution. In this Commentary, we focus on the recent developments and in situ applications of cryo-ET to cell and structural biology.
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Affiliation(s)
- Rossitza N. Irobalieva
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Bruno Martins
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, Beer-Sheva 84105, Israel
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Abstract
We acquired molecular-resolution structures of the Golgi within its native cellular environment. Vitreous Chlamydomonas cells were thinned by cryo-focused ion beam milling and then visualized by cryo-electron tomography. These tomograms revealed structures within the Golgi cisternae that have not been seen before. Narrow trans-Golgi lumina were spanned by asymmetric membrane-associated protein arrays that had ∼6-nm lateral periodicity. Subtomogram averaging showed that the arrays may determine the narrow central spacing of the trans-Golgi cisternae through zipper-like interactions, thereby forcing cargo to the trans-Golgi periphery. Additionally, we observed dense granular aggregates within cisternae and intracisternal filament bundles associated with trans-Golgi buds. These native in situ structures provide new molecular insights into Golgi architecture and function.
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Watté R, Aernouts B, Van Beers R, Herremans E, Ho QT, Verboven P, Nicolaï B, Saeys W. Modeling the propagation of light in realistic tissue structures with MMC-fpf: a meshed Monte Carlo method with free phase function. OPTICS EXPRESS 2015; 23:17467-86. [PMID: 26191756 DOI: 10.1364/oe.23.017467] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Monte Carlo methods commonly used in tissue optics are limited to a layered tissue geometry and thus provide only a very rough approximation for many complex media such as biological structures. To overcome these limitations, a Meshed Monte Carlo method with flexible phase function choice (fpf-MC) has been developed to function in a mesh. This algorithm can model the light propagation in any complexly shaped structure, by attributing optical properties to the different mesh elements. Furthermore, this code allows the use of different discretized phase functions for each tissue type, which can be simulated from the microstructural properties of the tissue, in combination with a tool for simulating the bulk optical properties of polydisperse suspensions. As a result, the scattering properties of tissues can be estimated from information on the microstructural properties of the tissue. This is important for the estimation of the bulk optical properties that can be used for the light propagation model, since many types of tissue have never been characterized in literature. The combination of these contributions, made it possible to use the MMC-fpf for modeling the light porapagation in plant tissue. The developed Meshed Monte Carlo code with flexible phase function choice (MMC-fpf) was successfully validated in simulation through comparison with the Monte Carlo code in Multi-Layered tissues (R2 > 0.9999) and experimentally by comparing the measured and simulated reflectance (RMSE = 0.015%) and transmittance (RMSE = 0.0815%) values for tomato leaves.
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Le Bihan T, Hindle M, Martin SF, Barrios-Llerena ME, Krahmer J, Kis K, Millar AJ, van Ooijen G. Label-free quantitative analysis of the casein kinase 2-responsive phosphoproteome of the marine minimal model species Ostreococcus tauri. Proteomics 2015; 15:4135-44. [PMID: 25930153 PMCID: PMC4716292 DOI: 10.1002/pmic.201500086] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 03/25/2015] [Accepted: 04/24/2015] [Indexed: 11/06/2022]
Abstract
Casein kinase 2 (CK2) is a protein kinase that phosphorylates a plethora of cellular target proteins involved in processes including DNA repair, cell cycle control, and circadian timekeeping. CK2 is functionally conserved across eukaryotes, although the substrate proteins identified in a range of complex tissues are often different. The marine alga Ostreococcus tauri is a unicellular eukaryotic model organism ideally suited to efficiently study generic roles of CK2 in the cellular circadian clock. Overexpression of CK2 leads to a slow circadian rhythm, verifying functional conservation of CK2 in timekeeping. The proteome was analysed in wild-type and CK2-overexpressing algae at dawn and dusk, revealing that differential abundance of the global proteome across the day is largely unaffected by overexpression. However, CK2 activity contributed more strongly to timekeeping at dusk than at dawn. The phosphoproteome of a CK2 overexpression line and cells treated with CK2 inhibitor was therefore analysed and compared to control cells at dusk. We report an extensive catalogue of 447 unique CK2-responsive differential phosphopeptide motifs to inform future studies into CK2 activity in the circadian clock of more complex tissues. All MS data have been deposited in the ProteomeXchange with identifier PXD000975 (http://proteomecentral.proteomexchange.org/dataset/PXD000975).
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Affiliation(s)
- Thierry Le Bihan
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Matthew Hindle
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Sarah F Martin
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Johanna Krahmer
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Katalin Kis
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Andrew J Millar
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Gerben van Ooijen
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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39
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Abstract
A shared feature among all microtubule (MT)-dependent processes is the requirement for MTs to be organized in arrays of defined geometry. At a fundamental level, this is achieved by precisely controlling the timing and localization of the nucleation events that give rise to new MTs. To this end, MT nucleation is restricted to specific subcellular sites called MT-organizing centres. The primary MT-organizing centre in proliferating animal cells is the centrosome. However, the discovery of MT nucleation capacity of the Golgi apparatus (GA) has substantially changed our understanding of MT network organization in interphase cells. Interestingly, MT nucleation at the Golgi apparently relies on multiprotein complexes, similar to those present at the centrosome, that assemble at the cis-face of the organelle. In this process, AKAP450 plays a central role, acting as a scaffold to recruit other centrosomal proteins important for MT generation. MT arrays derived from either the centrosome or the GA differ in their geometry, probably reflecting their different, yet complementary, functions. Here, I review our current understanding of the molecular mechanisms involved in MT nucleation at the GA and how Golgi- and centrosome-based MT arrays work in concert to ensure the formation of a pericentrosomal polarized continuous Golgi ribbon structure, a critical feature for cell polarity in mammalian cells. In addition, I comment on the important role of the Golgi-nucleated MTs in organizing specialized MT arrays that serve specific functions in terminally differentiated cells.
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Affiliation(s)
- Rosa M Rios
- Cell Signalling Department, CABIMER-CSIC, Seville 41092, Spain
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40
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Tang WG, Song P, Cao ZY, Wang P, Zhu GP. A unique homodimeric NAD⁺-linked isocitrate dehydrogenase from the smallest autotrophic eukaryote Ostreococcus tauri. FASEB J 2015; 29:2462-72. [PMID: 25724193 DOI: 10.1096/fj.14-257014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 02/03/2015] [Indexed: 11/11/2022]
Abstract
In eukaryotes, NAD(+)-dependent isocitrate dehydrogenase (IDH) is strictly mitochondrial and is a key enzyme in the Krebs cycle. To date, all known NAD(+)-specific IDHs (NAD-IDHs) in the mitochondria are believed to be heteromeric in solution. Here, a unique homodimeric NAD-IDH from Ostreococcus tauri (OtIDH), the smallest autotrophic picoeukaryote, was unveiled. Active OtIDH has a molecular weight of ∼93 kDa with each subunit of 46.7 kDa. In the presence of Mn(2+) and Mg(2+), OtIDH displayed 42-fold and 51-fold preference for NAD(+) over NADP(+), respectively. Interestingly, OtIDH exhibited a sigmoidal kinetic behavior in response to isocitrate unlike other homodimeric homologs, and a remarkably high affinity for isocitrate (S0.5 < 10 μM) unlike other hetero-oligomeric homologs. Furthermore, its coenzyme specificity can be completely converted from NAD(+) (ancient trait) to NADP(+) (adaptive trait) by rational mutagenesis based on the evolutionary trace. Mutants D344R and D344R/M345H displayed a 15-fold and 72-fold preference for NADP(+) over NAD(+), respectively, indicating that D344 and M345 are the determinants of NAD(+) specificity. These findings also suggest that OtIDH may be an ancestral form of type II IDHs (all reported members are NADP(+)-linked enzymes) and may have evolved into NADP(+)-dependent IDH for adaptation to the increased demand of NADPH under carbon starvation.
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Affiliation(s)
- Wang-Gang Tang
- Institute of Molecular Biology and Biotechnology, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Ping Song
- Institute of Molecular Biology and Biotechnology, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Zheng-Yu Cao
- Institute of Molecular Biology and Biotechnology, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Peng Wang
- Institute of Molecular Biology and Biotechnology, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Guo-Ping Zhu
- Institute of Molecular Biology and Biotechnology, College of Life Sciences, Anhui Normal University, Wuhu, China
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41
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Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae. Proc Natl Acad Sci U S A 2015; 112:2314-9. [PMID: 25675478 DOI: 10.1073/pnas.1413003112] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Trace metals play important roles in normal and in disease-causing biological functions. X-ray fluorescence microscopy reveals trace elements with no dependence on binding affinities (unlike with visible light fluorophores) and with improved sensitivity relative to electron probes. However, X-ray fluorescence is not very sensitive for showing the light elements that comprise the majority of cellular material. Here we show that X-ray ptychography can be combined with fluorescence to image both cellular structure and trace element distribution in frozen-hydrated cells at cryogenic temperatures, with high structural and chemical fidelity. Ptychographic reconstruction algorithms deliver phase and absorption contrast images at a resolution beyond that of the illuminating lens or beam size. Using 5.2-keV X-rays, we have obtained sub-30-nm resolution structural images and ∼90-nm-resolution fluorescence images of several elements in frozen-hydrated green algae. This combined approach offers a way to study the role of trace elements in their structural context.
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42
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Roll, adhere, spread and contract: structural mechanics of platelet function. Eur J Cell Biol 2015; 94:129-38. [PMID: 25655000 DOI: 10.1016/j.ejcb.2015.01.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 12/26/2014] [Accepted: 01/07/2015] [Indexed: 12/31/2022] Open
Abstract
Platelets are involved in life-sustaining processes such as hemostasis, wound healing, atherothrombosis and angiogenesis. Mechanical trauma to blood vessels causes platelet activation resulting in their adherence and clot formation at the damaged site, culminating in clot retraction and tissue repair. Two of the major players underlying this process are the cytoskeleton, i.e., actin and microtubules, and the membrane integrin receptors. Rare congenital bleeding disorders such as Glanzmann thrombasthenia and Bernard-Soulier syndrome are associated with genetic alterations of platelet surface receptors, also affecting the platelet cytoskeletal structure. In this review, we summarize the current knowledge about platelet structure and adhesion, and delve into the mechanical aspects of platelet function. Platelets lack a nucleus, and can thus provide a minimal model of a biological cell. New biophysical tools may help to scrutinize platelets anew and to extend the existing knowledge on cell biology.
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43
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Engel BD, Schaffer M, Kuhn Cuellar L, Villa E, Plitzko JM, Baumeister W. Native architecture of the Chlamydomonas chloroplast revealed by in situ cryo-electron tomography. eLife 2015; 4. [PMID: 25584625 PMCID: PMC4292175 DOI: 10.7554/elife.04889] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/08/2014] [Indexed: 12/19/2022] Open
Abstract
Chloroplast function is orchestrated by the organelle's intricate architecture. By combining cryo-focused ion beam milling of vitreous Chlamydomonas cells with cryo-electron tomography, we acquired three-dimensional structures of the chloroplast in its native state within the cell. Chloroplast envelope inner membrane invaginations were frequently found in close association with thylakoid tips, and the tips of multiple thylakoid stacks converged at dynamic sites on the chloroplast envelope, implicating lipid transport in thylakoid biogenesis. Subtomogram averaging and nearest neighbor analysis revealed that RuBisCO complexes were hexagonally packed within the pyrenoid, with ∼15 nm between their centers. Thylakoid stacks and the pyrenoid were connected by cylindrical pyrenoid tubules, physically bridging the sites of light-dependent photosynthesis and light-independent carbon fixation. Multiple parallel minitubules were bundled within each pyrenoid tubule, possibly serving as conduits for the targeted one-dimensional diffusion of small molecules such as ATP and sugars between the chloroplast stroma and the pyrenoid matrix. DOI:http://dx.doi.org/10.7554/eLife.04889.001 Many organisms can harvest light to produce their own energy through a process called photosynthesis. In plant and algal cells, photosynthesis takes place within the chloroplasts, which are compartments that contain stacks of structures called thylakoids. Inside the thylakoids, proteins absorb energy from light and convert it into biochemical energy that can be used by the cell. This energy then powers a series of reactions that result in carbon dioxide being incorporated into energy-rich sugars. The enzyme RuBisCO is essential for this process, and is believed to be the most abundant protein on Earth. In land plants, RuBisCO is found throughout the chloroplast, but in algae it is limited to a specialized area called the pyrenoid. Much of our current knowledge of chloroplast structure comes from transmission electron microscopy (TEM) images. However, the traditional methods used to prepare cells for TEM can damage their internal structures. Also, previous studies have focused primarily on the chloroplasts of land plants, even though aquatic organisms—including the alga Chlamydomonas—account for over 50% of photosynthesis on the planet. Here, Engel et al. provide the first three-dimensional structures of Chlamydomonas chloroplasts in their natural state. They used several recently-developed techniques to study cells that were preserved in a close-to-living condition. The cells were rapidly frozen, thinned with a technique called cryo-focused ion beam milling, and then imaged by a type of TEM called cryo-electron tomography. The three-dimensional images provide many insights into the Chlamydomonas chloroplast, including evidence that lipids and proteins move between the membrane that surrounds the chloroplast—called the chloroplast envelope—and the tips of the thylakoids. These images show how thylakoids may be built by the transport of molecules from the chloroplast envelope. In addition, the images reveal the detailed structures of the tubes that connect the thylakoids to the pyrenoid, which could explain how the two stages of photosynthesis (light harvesting and the conversion of carbon dioxide) can be coordinated even though they occur at different places within the chloroplast. Engel et al. also observed that RuBisCO enzymes are arranged in a hexagonal pattern inside the pyrenoid, but are spaced too far apart to make direct contact with each other. To understand how the pyrenoid is assembled, a future goal will be to determine what causes RuBisCO to be arranged in this way. DOI:http://dx.doi.org/10.7554/eLife.04889.002
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Affiliation(s)
- Benjamin D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Luis Kuhn Cuellar
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Elizabeth Villa
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
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44
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Engel BD, Schaffer M, Kuhn Cuellar L, Villa E, Plitzko JM, Baumeister W. Native architecture of the Chlamydomonas chloroplast revealed by in situ cryo-electron tomography. eLife 2015. [PMID: 25584625 DOI: 10.7554/elife.04889#sthash.yy91intr.dpuf] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chloroplast function is orchestrated by the organelle's intricate architecture. By combining cryo-focused ion beam milling of vitreous Chlamydomonas cells with cryo-electron tomography, we acquired three-dimensional structures of the chloroplast in its native state within the cell. Chloroplast envelope inner membrane invaginations were frequently found in close association with thylakoid tips, and the tips of multiple thylakoid stacks converged at dynamic sites on the chloroplast envelope, implicating lipid transport in thylakoid biogenesis. Subtomogram averaging and nearest neighbor analysis revealed that RuBisCO complexes were hexagonally packed within the pyrenoid, with ~15 nm between their centers. Thylakoid stacks and the pyrenoid were connected by cylindrical pyrenoid tubules, physically bridging the sites of light-dependent photosynthesis and light-independent carbon fixation. Multiple parallel minitubules were bundled within each pyrenoid tubule, possibly serving as conduits for the targeted one-dimensional diffusion of small molecules such as ATP and sugars between the chloroplast stroma and the pyrenoid matrix.
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Affiliation(s)
- Benjamin D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Luis Kuhn Cuellar
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Elizabeth Villa
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
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45
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Guerriero ML, Akman OE, van Ooijen G. Stochastic models of cellular circadian rhythms in plants help to understand the impact of noise on robustness and clock structure. FRONTIERS IN PLANT SCIENCE 2014; 5:564. [PMID: 25374576 PMCID: PMC4204444 DOI: 10.3389/fpls.2014.00564] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 09/30/2014] [Indexed: 05/25/2023]
Abstract
Rhythmic behavior is essential for plants; for example, daily (circadian) rhythms control photosynthesis and seasonal rhythms regulate their life cycle. The core of the circadian clock is a genetic network that coordinates the expression of specific clock genes in a circadian rhythm reflecting the 24-h day/night cycle. Circadian clocks exhibit stochastic noise due to the low copy numbers of clock genes and the consequent cell-to-cell variation: this intrinsic noise plays a major role in circadian clocks by inducing more robust oscillatory behavior. Another source of noise is the environment, which causes variation in temperature and light intensity: this extrinsic noise is part of the requirement for the structural complexity of clock networks. Advances in experimental techniques now permit single-cell measurements and the development of single-cell models. Here we present some modeling studies showing the importance of considering both types of noise in understanding how plants adapt to regular and irregular light variations. Stochastic models have proven useful for understanding the effect of regular variations. By contrast, the impact of irregular variations and the interaction of different noise sources are less well studied.
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Affiliation(s)
| | - Ozgur E. Akman
- Centre for Systems, Dynamics and Control, College of Engineering, Mathematics and Physical Sciences, University of ExeterExeter, UK
| | - Gerben van Ooijen
- Institute of Molecular Plant Sciences, University of EdinburghEdinburgh, UK
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46
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Hindle MM, Martin SF, Noordally ZB, van Ooijen G, Barrios-Llerena ME, Simpson TI, Le Bihan T, Millar AJ. The reduced kinome of Ostreococcus tauri: core eukaryotic signalling components in a tractable model species. BMC Genomics 2014; 15:640. [PMID: 25085202 PMCID: PMC4143559 DOI: 10.1186/1471-2164-15-640] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 07/08/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The current knowledge of eukaryote signalling originates from phenotypically diverse organisms. There is a pressing need to identify conserved signalling components among eukaryotes, which will lead to the transfer of knowledge across kingdoms. Two useful properties of a eukaryote model for signalling are (1) reduced signalling complexity, and (2) conservation of signalling components. The alga Ostreococcus tauri is described as the smallest free-living eukaryote. With less than 8,000 genes, it represents a highly constrained genomic palette. RESULTS Our survey revealed 133 protein kinases and 34 protein phosphatases (1.7% and 0.4% of the proteome). We conducted phosphoproteomic experiments and constructed domain structures and phylogenies for the catalytic protein-kinases. For each of the major kinases families we review the completeness and divergence of O. tauri representatives in comparison to the well-studied kinomes of the laboratory models Arabidopsis thaliana and Saccharomyces cerevisiae, and of Homo sapiens. Many kinase clades in O. tauri were reduced to a single member, in preference to the loss of family diversity, whereas TKL and ABC1 clades were expanded. We also identified kinases that have been lost in A. thaliana but retained in O. tauri. For three, contrasting eukaryotic pathways - TOR, MAPK, and the circadian clock - we established the subset of conserved components and demonstrate conserved sites of substrate phosphorylation and kinase motifs. CONCLUSIONS We conclude that O. tauri satisfies our two central requirements. Several of its kinases are more closely related to H. sapiens orthologs than S. cerevisiae is to H. sapiens. The greatly reduced kinome of O. tauri is therefore a suitable model for signalling in free-living eukaryotes.
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Affiliation(s)
| | | | | | | | | | | | | | - Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JD, UK.
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47
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Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell 2014; 156:1286-1297. [PMID: 24630728 DOI: 10.1016/j.cell.2014.01.029] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 10/25/2013] [Accepted: 01/10/2014] [Indexed: 11/24/2022]
Abstract
Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.
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48
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Mironov AA. ER-Golgi transport could occur in the absence of COPII vesicles. Nat Rev Mol Cell Biol 2014; 15:1. [PMID: 24496389 DOI: 10.1038/nrm3588-c1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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49
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Han HM, Bouchet-Marquis C, Huebinger J, Grabenbauer M. Golgi apparatus analyzed by cryo-electron microscopy. Histochem Cell Biol 2013; 140:369-81. [PMID: 23954988 PMCID: PMC3787787 DOI: 10.1007/s00418-013-1136-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2013] [Indexed: 11/28/2022]
Abstract
In 1898, the Golgi apparatus was discovered by light microscopy, and since the 1950s, the ultrastructure composition is known by electron microscopic investigation. The complex three-dimensional morphology fascinated researchers and was sometimes even the driving force to develop novel visualization techniques. However, the highly dynamic membrane systems of Golgi apparatus are delicate and prone to fixation artifacts. Therefore, the understanding of Golgi morphology and its function has been improved significantly with the development of better preparation methods. Nowadays, cryo-fixation is the method of choice to arrest instantly all dynamic and physiological processes inside cells, tissues, and small organisms. Embedded in amorphous ice, such samples can be further processed by freeze substitution or directly analyzed in their fully hydrated state by cryo-electron microscopy and tomography. Even though the overall morphology of vitrified Golgi stacks is comparable to well-prepared and resin-embedded samples, previously unknown structural details can be observed solely based on their native density. At this point, any further improvement of sample preparation would gain novel insights, perhaps not in terms of general morphology, but on fine structural details of this dynamic organelle.
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Affiliation(s)
- Hong-Mei Han
- Department of Systemic Cell Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Cedric Bouchet-Marquis
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO USA
- FEI Company, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124 USA
| | - Jan Huebinger
- Department of Systemic Cell Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Markus Grabenbauer
- Institute of Anatomy and Cell Biology, Heidelberg University, INF 307, 69120 Heidelberg, Germany
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50
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Subirana L, Péquin B, Michely S, Escande ML, Meilland J, Derelle E, Marin B, Piganeau G, Desdevises Y, Moreau H, Grimsley NH. Morphology, Genome Plasticity, and Phylogeny in the Genus Ostreococcus Reveal a Cryptic Species, O. mediterraneus sp. nov. (Mamiellales, Mamiellophyceae). Protist 2013; 164:643-59. [PMID: 23892412 DOI: 10.1016/j.protis.2013.06.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Revised: 05/27/2013] [Accepted: 06/18/2013] [Indexed: 01/16/2023]
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